[Bioc-devel] upgrading

[Kasper Daniel Hansen]

Thanks for all the help.  Indeed, removing BiocInstaller and then sourcing
biocLite made it all work.

Martin: I am updating R-devel daily by building from subversion (building
in a fresh directory, but installing on top of an existing installation),
but anything from Bioconductor comes through biocLite only.

Given that the fix is easy, it is not clear it is worth spending any energy
on this.  But it is a bit weird that running R-devel with BiocInstaller
1.20.0 installed and then sourcing biocLite.R does not detect that a newer
version can be obtained.

There also seems to be something specific to R-devel here.  I was running
  R-3.2-pached
  R-devel
both with BiocInstaller 1.19.x (pre-bioc-3.2-release).  After the Bioc 3.2
release I could run
  biocLite("BiocUpgrade")
and everything would be upgraded (and working) for R-3.2-patched (upgrading
to BiocInstaller 1.20.0 / Bioc-3.2).  For R-devel it would upgrade to
BiocInstaller 1.20.0 as well, but I could not get the last version bump
without deleting and re-installing.

Weird, but as I said, perhaps not worth spending time on since the fix is
so easy.

Best,
Kasper

On Tue, Oct 20, 2015 at 11:45 AM, Morgan, Martin <
Martin.Morgan at roswellpark.org> wrote:

> Technically, prior to the release we were using R-3.2 for both release and
> devel. Only after the release did we 'support' R-devel, implying a new
> installation of BiocInstaller.
>
> I guess you were using R-devel prior to the release and had an unsupported
> installation of BiocInstaller. Alternatively, you updated R over an
> existing library. Apparently at least one of these scenarios (probably the
> former) is somehow common amongst Bioc developers. I guess in general our
> approach has been to realize that there are many incorrect ways to skin a
> cat, and we cannot possibly anticipate all of them, so we will only support
> the approved way.
>
> Sorry for the frustration.
>
> Martin
>
> > -----Original Message-----
> > From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
> > Kasper Daniel Hansen
> > Sent: Tuesday, October 20, 2015 10:55 AM
> > To: bioc-devel at r-project.org
> > Subject: [Bioc-devel] upgrading
> >
> > So I have an R-devel where I have a previous (pre-bioc-3.2) installed
> version
> > of BiocInstaller.
> >
> > 1) I re-compile R-devel today.
> > 2) I run
> >   source("http://www.bioconductor.org/biocLite.R")
> > which gives me BiocInstaller 1.20.0.  However, the current one for
> Bioc-devel
> > is 1.21.1.
> >
> > When I try to push to a higher level version, by doing
> >   library(BiocInstaller)
> >   useDevel(TRUE)
> > I get
> >
> > > useDevel(TRUE)
> > Error: 'devel' version requires a more recent R
> >
> > If I now try to upgrade I get
> > > biocLite("BiocUpgrade")
> > Error: Bioconductor version 3.2 cannot be upgraded with R version 3.3.0
> >
> > This all looks problematic.  How to I upgrade to Bioc-devel using
> R-devel?
> > Btw. there are no instructions anymore at
> >   https://www.bioconductor.org/developers/how-to/useDevel/
> >
> > Best,
> > Kasper
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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